I have two folders: notes/ and uploads/. I've been uploading any attachments (images, PDFs, etc) to uploads/ with a timestamped name (ex. "2018-07-15_interesting_document.pdf") and linking them from the associated note.

At first this was pretty annoying, but then I wrote a couple scripts to automate the upload + naming process. Now it's as simple as running the script and getting the Markdown reference copied to your clipboard (ex. "").